Study of the Formation of Nano-Networks in Colloidal Particles

The authors studied the formation of a wafer-scale network of connected colloidal beads by reactive ion etching. The dimensions of the connections have been studied as a function of etching time for colloidal beads of different sizes, and could be well controlled. The authors have found that the nano-network forms and disappears for the same time of etching independent of the diameter of the polystyrene beads. With recent interest of connected colloidal networks in various optical sensing applications, such as photonic crystals, as surface-enhanced Raman scattering substrates, the studies have potential uses in the development of wafer-scale nanophotonic sensors.

Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of mycobacterium tuberculosis

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of Mycobacterium tuberculosis, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in Mycobacterium smegmatis resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.

Towards the understanding of formation of micro/nano holes of Ge/GeO2 through phase mapping

Here, we report for the first time a simple thermal oxidation strategy for the large area synthesis of Ge/GeO2 nanoholes from Ge and studied the luminescence of Ge/GeO2 and hole formation mechanism through phase and luminescence mapping. Photoluminescence mapping reveals that the emission in the visible range is only from the hole region, which provokes the necessity of the nanoholes. Such materials can also be used to convert ultraviolet to visible radiation for detection by conventional phototubes and to coat blue or ultraviolet diodes to obtain white light.

Spontaneous formation of branched nanochains from room temperature molten amides: visible and near-IR active, SERS substrates for non-fluorescent and fluorescent analytes

Highly stable, branched gold nanoworms are formed spontaneously in an acetamide-based room temperature molten solvent without any additional external stabilizing or aggregating agent. The nanoworms can be anchored onto solid substrates such as indium tin oxide (ITO) without any change in morphology. The anchored nanoworms are explored as substrates for surface enhanced Raman scattering (SERS) studies using non-fluorescent 4-mercaptobenzoic acid (4-MBA) and fluorescent rhodamine 6G (R6G) as probe molecules. The anchored nanostructured particles respond to near IR (1064 nm) as well as visible (785, 632.8 and 514 nm) excitation lasers and yield good surface enhancement in Raman signals. Enhancement factors of the order 10(6)-10(7) are determined for the analytes using a 1064 nm excitation source. Minimum detection limits based on adsorption from ethanolic solutions of 1028 M 4-MBA and aqueous solutions of 1027 M R6G are achieved. Experimental Raman frequencies and frequencies estimated by DFT calculations are in fairly good agreement. SERS imaging of the nanostructures suggests that the substrates comprising of three dimensional, highly interlinked particles are more suited than particles fused in one dimension. The high SERS activity of the branched nanoworms may be attributed to both electromagnetic and charge transfer effects.

Determination of favorable inter-particle interactions for formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

The solid phase formed by a binary mixture of oppositely charged colloidal particles can be either substitutionally ordered or substitutionally disordered depending on the nature and strength of interactions among the particles. In this work, we use Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique to map out the favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase. The inter-particle interactions are modeled using the hard core Yukawa potential but the method can be easily extended to other systems of interest. The study obtains a map of interactions depicting regions indicating the type of the crystalline aggregate that forms upon phase transition.

Gibbs energy of formation of Ca7V4O17

Thermodynamic properties of Ca7V4O17 are measured for the first time using a solid-state electrochemical cell incorporating single crystal of CaF2 as the electrolyte over the temperature range from (900 to 1175) K. An equimolar mixture of CaO and CaF2 is used as the reference electrode and a mixture of Ca3V2O8, Ca7V4O17 and CaF2 as the measuring electrode. Both the electrodes are placed under flowing oxygen gas at ambient pressure. The standard Gibbs energy change for the reaction: 2Ca(3)V(2)O(8) + CaO -> Ca7V4O17; which is related to the chemical potential of CaO in the two-phase region (Ca3V2O8 + Ca7V4O17) of the pseudo-binary system CaO + V2O5, is obtained from the electromotive force of the cell as: Delta(r)G(o) +/- 127/(J . mol(-1)) = Delta mu(CaO) = -11453 + 8.273(T/K). The derived standard enthalpy of formation of Ca7V4O17 from elements in their normal standard states is ( 8208.97 +/- 8) kJ . mol (1) and its standard entropy is (560.05 +/- 7.5) J . K (1) . mol (1), both at T = 298.15 K. The results indicate that Ca7V4O17 decomposes into Ca3V2O8 and CaO at T = (1384 +/- 3) K.

Black hole formation at the correspondence point

We study the process of bound state formation in a D-brane collision. We consider two mechanisms for bound state formation. The first, operative at weak coupling in the worldvolume gauge theory, is pair creation of W-bosons. The second, operative at strong coupling, corresponds to formation of a large black hole in the dual supergravity. These two processes agree qualitatively at intermediate coupling, in accord with the correspondence principle of Horowitz and Polchinski. We show that the size of the bound state and time scale for formation of a bound state agree at the correspondence point. The time scale involves matching a parametric resonance in the gauge theory to a quasinormal mode in supergravity.

Unprecedented formation of a 14-membered dihydropyran macrocycle via sequential olefin cross metathesis-intramolecular hetero Diels-Alder reaction

Formation of a 2,3-dihydro-4H-pyran containing 14-membered macrocycle by sequential olefin cross metathesis and a highly regiospecific hetero Diels-Alder reaction was observed in the reaction of a hydroxydienone derived from tartaric acid with Grubbs' second generation catalyst. It was found that the free alcohol in the hydroxyenone led to the macrocycle formation, while protection of the hydroxy group formed the ring closing metathesis product. (C) 2013 Elsevier Ltd. All rights reserved.

Organogels from Dimeric Bile Acid Esters: In Situ Formation of Gold Nanoparticles

A new class of steroid dimers (bile acid derivatives) linked through ester functionalities were synthesized, which gelled various aromatic solvents. The organogels formed by the three dimeric ester molecules showed birefringent textures and fibrous nature by polarizing optical microscopy and scanning electron microscopy, respectively. A detailed rheological study was performed to estimate the mechanical strengths of two sets of organogels. In these systems, the storage modulus varied in the range of 0.8-3.5 X 10(4) at 1% w/v of the organogelators. The exponents of scaling of the storage modulus and yield stress of the two systems agreed well with those expected for viscoelastic soft colloidal gels with fibrillar flocs. The nanofibers in the organogel were utilized to engineer gold nanoparticles of different sizes and shapes and generate new gel-nanoparticle hybrid materials.

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence

While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.

Black hole formation in fuzzy sphere collapse

We study the collapse of a fuzzy sphere, that is a spherical membrane built out of D0-branes, in the Banks-Fischler-Shenker-Susskind model. At weak coupling, as the sphere shrinks, open strings are produced. If the initial radius is large then open string production is not important and the sphere behaves classically. At intermediate initial radius the backreaction from open string production is important but the fuzzy sphere retains its identity. At small initial radius the sphere collapses to form a black hole. The crossover between the later two regimes is smooth and occurs at the correspondence point of Horowitz and Polchinski.

Note: Effect of fluid phase compositions on the formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

A binary mixture of oppositely charged colloidal particles can self-assemble into either a substitutionally ordered or substitutionally disordered crystalline phase depending on the nature and strength of interactions among the particles. An earlier study had mapped out favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase using Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique. In this paper, those studies are extended to determine the effect of fluid phase composition on formation of substitutionally ordered solid phases.

N-Terminal disordered domain of saccharomyces cerevisiae Hop1 protein Is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is ecessary for spore formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.

The Modified Selenenyl Amide, M-hydroxy Ebselen, Attenuates Diabetic Nephropathy and Diabetes-Associated Atherosclerosis in ApoE/GPx1 Double Knockout Mice

Seleno-organic glutathione peroxidase (GPx) mimetics, including ebselen (Eb), have been tested in in vitro studies for their ability to scavenge reactive oxygen and nitrogen species, including hydrogen peroxide and peroxynitrite. In this study, we investigated the efficacies of two Eb analogues, m-hydroxy ebselen (ME) and ethanol-ebselen (EtE) and compared these with Eb in cell based assays. We found that ME is superior in attenuating the activation of hydrogen peroxide-induced pro-inflammatory mediators, ERK and P38 in human aortic endothelial cells. Consequently, we investigated the effects of ME in an in vivo model of diabetes, the ApoE/GPx1 double knockout (dKO) mouse. We found that ME attenuates plaque formation in the aorta and lesion deposition within the aortic sinus of diabetic dKO mice. Oxidative stress as assessed by 8-OHdG in urine and nitrotyrosine immunostaining in the aortic sinus and kidney tubules, was reduced by ME in diabetic dKO mice. ME also attenuated diabetes-associated renal injury which included tubulointerstitial fibrosis and glomerulosclerosis. Furthermore, the bioactivity of the pro-fibrotic cytokine transforming growth factor-beta (TGF-beta) as assessed by phospho-Smad2/3 immunostaining was attenuated after treatment with ME. TGF-beta-stimulated increases in collagen I and IV gene expression and protein levels were attenuated by ME in rat kidney tubular cells. However, in contrast to the superior activity of ME in in vitro and cell based assays, ME did not further augment the attenuation of diabetes-associated atherosclerosis and renal injury in our in vivo model when compared with Eb. In conclusion, this study strengthens the notion that bolstering GPx-like activity using synthetic mimetics may be a useful therapeutic strategy in lessening the burden of diabetic complications. However, these studies highlight the importance of in vivo analyses to test the efficacies of novel Eb analogues, as in vitro and cell based assays are only partly predictive of the in vivo situation.